ArticleCell reports methods2025
Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues.
Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Immunophenotyping by Single-Cell CITE-Seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Cell-based therapies of autoimmune diseases in the context of artificial intelligence development.Clinical and experimental medicine · 2026Review
- Distinct transcription factors control tissue adaptation and effector function in infant and adult memory T cells.Nature immunology · 2026Article
- Age determines NK cell fate and tissue compartmentalization to CMV infection.bioRxiv : the preprint server for biology · 2026Article
- Tissue signatures of human macrophages during homeostasis and activation.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- ImmunoPheno: A Computational Framework for Data-Driven Design and Analysis of Immunophenotyping Experiments.bioRxiv : the preprint server for biology · 2026Article
- Advances in the pathophysiological study of brain development: application of cerebral organoid combined with Spatial omics technology.Stem cell research & therapy · 2026Review
- Lung tissue-resident memory T cells optimize protection by IL-10 regulation of innate immunity.The Journal of experimental medicine · 2026Article
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- The normal human lymph node cell classification and landscape defined by high-dimensional spatial proteomics.PloS one · 2026Article
- The evolving role of the immune microenvironment of tumor draining lymph nodes in the development of biomarkers of non-small cell lung cancer.Frontiers in oncology · 2026Review
- CD8⁺ T cell heterogeneity in aging: insights from single-cell profiling.Immunity & ageing : I & A · 2025Review
- A unified multimodal single-cell framework reveals a discrete state model of hematopoiesis in mice.Nature immunology · 2025Article
- Proximity and metabolic activity proxies in the tumor microenvironment as predictors of survival in high grade serous ovarian cancer.iScience · 2025Article
- Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.Nature immunology · 2025Article
- Sketching T cell atlases in the single-cell era: challenges and recommendations.Immunology and cell biology · 2025Review
- Automated denoising of CITE-seq data with ThresholdR.Cell reports methods · 2025Article
- scDCT: a conditional diffusion-based deep learning model for high-fidelity single-cell cross-modality translation.Briefings in bioinformatics · 2025Article
- ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets.Nature communications · 2025Article
- The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment.NPJ precision oncology · 2025Article
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Abstract
Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins. Cellular indexing of transcriptomes and epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes; however, accurate cell-type annotation requires a classifier that integrates multimodal data. Here, we describe multimodal classifier hierarchy (MMoCHi), a marker-based approach for accurate cell-type classification across multiple single-cell modalities that does not rely on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal subset markers. MMoCHi is designed for adaptability and can integrate annotation of cell types and developmental states across diverse lineages, samples, or modalities.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.